Distribution of all splicing index values that meet the SI cutoff (indicated by red dotted lines) for the feature type: SilentIntronRegion. The total number of features with SI values exceeding the cutoff, as well as the max and min log2 SI observed are noted in the legend. *If you can not see the figure below, click here

Significant alternatively expressed SilentIntronRegion features

The following table provides a ranked list of alternatively expressed SilentIntronRegion features for a single pair-wise library comparison. The first column contains the Gene Name (which links to the ALEXA-Seq gene record), the Feature Name, and the name of each library being compared (which links to the feature's coordinates in the UCSC Genome Browser and displays expression data). The 'SI' column reports the Splicing Index calculated for the feature. The 'Gene FC' column reports the Fold-Change calculated for the entire gene to which the feature belongs. The 'Seq FC' column reports the Fold-Change of the feature itself. The 'Reciprocity' column reports the Reciprocity Index (RI) for the feature. The 'Percent Seq DE' column reports the Percent Feature Contribution (PFC) value for the feature. A description of the purpose and calculation of SI, RI and PFC values can be found in our manuscript. Briefly, the SI value is a measure of the degree of change in expression of a feature (e.g. an exon) between two conditions relative to the change in expression at the gene level. The RI value is a measure of the degree to which the change of the feature is reciprocal in direction to that observed for the gene overall. For example, if an exon is up-regulated but the gene overall is down-regulated, this will give a higher RI value. The PFC value is a measure of the degree of differential expression of the feature compared to the entire gene. For example, if a gene is not changed overall between two conditions, but the feature is highly differentially expressed, this will give a higher PFC value. To sort this table by each of the data values, simply click the column header. A bold row indicates that the feature is not currently supported by EST or mRNA sequence alignments. For exon junction features the number of exons skipped by the junction is indicated as 'Sn' where n is the number of exons skipped (e.g. S0 means no exons skipped, S1 means one exon skipped, etc.).